This paper presents a surface motor-driven multi-axis stage system employing a surface encoder as the position feedback sensor. The surface motor consists of four two-phase linear motors, two pairs in X- and Y-directions. The thrust force generated by each of the linear motor's two phases was investigated for the purpose of constructing dynamic controller of the stage. It was confirmed that the thrust forces of the two phases were sinusoidal functions of positions with a shift in space by one-quarter of the motor pitch length of 5 mm. A simple commutation law was applied to the two-phase forces so that a constant force can be obtained throughout the full range of travel. A PC-based PID controller was designed and constructed for micro-positioning experiments of the stage. Experimental results indicated that dynamic micro-positioning can be carried out independently in X and Y-axes with a positioning resolution of 50 nm.